I strongly endorse Judd's point here. Linking characters doesn't necessarily make a huge difference to the mission structure as such, but it does alter the way characters and players approach the mission, and thepertinence of individual character identities.

When characters are unrelated, the mission has to be built in a way that provides motivation for all of them; this means it must also be impersonal. Furthermore, there is a constant undertone of dispute over "my character isn't interested in doing X or Y" that has to be constantly negotiated. All of which results in one of two outcomes: either the players are fractious and difficult, or they ignore their character identities for the sake of party unity.

I introduced a rule to a group that played in much the way you describe, and it completely transformed this situation. Characters didn't have to be created in full with the others, but the basic concepts had to be discussed with others, and each character had to have one non-reciprocal link to another character. This creates a network of interdepency among the characters and thus players and gives them, as well as the GM, an explicit framework in which to interact with each other.

So, your Crane bushi as character A might say, I am the "brother of character B", but character B cannot then have a link back to A; this player must construct a link to character C, like "the Daidoji is my personal bodyguard". Once a network like this is established, the motivation problem for missions becomes much simpler - all you have to do is tug on one character, and all the others are affected. In addition, all the "my character wouldn't do that" stuff vanishes, because now each character is equipped with a Reason for doing stuff about which they may well have misgivings, but which they are none the less obliged to do by ties of loyalty, dependency, familial relation, etc. Motivation and involvement thus cease to be abstract concerns and become things negotiated between players through the playing of characters. Which itself has the function of making characters more "alive" and realised in the SIS.

It also makes the characters more of a unit, not in the sense they all have shared motives, but in the sense that they are all mutually affecting. And that in turn opens up space for players to initiate things that are primarily of concern only to their own characters, but which nevertheless involve and have implications for the others. that both reduces the amount of stuff that is of exclusive interest to only one at a time, and allows for a natural interest and involvement by the others, while also preserving an interest among the players in something that is executed as a one character scene.

Thanks people. If nothing else, this thread's reminded me about what worked in certain games in the past. If anyone has further techniques or devices to share in regards to establishing more 'links' between characters, prepping games for such characters, encouraging more player interaction and communication during chargen, or any thoughts on how to convert a game that was conceived with a lack of attention to such (eg, our current games), please post away.